Sun Oct 9 17:12:27 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 17:12:27 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4671 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5879730 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 2.923000 61.76500 ymin,ymax (A): -8.835000 51.71200 zmin,zma (A): -1.957000 57.47600 x,y,z range (A): 58.84200 60.54700 59.43300 scale (grids/A): 0.5879730 object centre (A): 32.34400 21.43850 27.75950 number of atom coordinates read : 4671 total number of charged atoms : 4557 net assigned charge : -0.3649497 assigned positive charge : 723.6348 centred at (gu) : 88.78438 89.48923 90.18427 assigned negative charge : -724.0048 centred at (gu) : 88.69419 89.51411 90.13982 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 10737 nv = 96 ne = 84 npr = 93901 no. pairs analyzed = 93901 no. exposed pairs = 5501 no. arc points = 37192 no. surface atoms = 1886 nbur = 2785 mkacc time = 0.2200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 519 mr = 6197 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 5010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3884 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 13842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0424014E-09 2.0859536E-09 midg,1,midg; midg,igrid,midg 1.2372655E-09 -1.0797362E-09 1,midg,midg; igrid,midg,midg -5.7267275E-09 3.0768466E-09 gauss-seidel spectral radius is 0.9851971 estimated iterations to convergence 67 setup time was (sec) 0.7200000 now iterating at: 17:12:28 rms-change max change #iterations 0.1427694 16.56793 at 10iterations 1.3100883E-02 1.712051 at 20iterations 2.7278305E-03 0.2979889 at 30iterations 1.1375381E-03 0.1165378 at 40iterations 5.2011403E-04 5.8914185E-02 at 50iterations finished qdiffx linear iterations at : 17:12:31 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 5.2011403E-04 5.8914185E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 17:12:31 3.550u 0.142s 0:03.96 93.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 17:12:31 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4671 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.763919 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 2.923000 61.76500 ymin,ymax (A): -8.835000 51.71200 zmin,zma (A): -1.957000 57.47600 x,y,z range (A): 58.84200 60.54700 59.43300 scale (grids/A): 1.763919 object centre (A): 32.34400 21.43850 27.75950 number of atom coordinates read : 4671 total number of charged atoms : 4557 net assigned charge : -0.3649497 assigned positive charge : 723.6348 centred at (gu) : 86.35190 88.46659 90.55161 assigned negative charge : -724.0048 centred at (gu) : 86.08226 88.54263 90.41927 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 118316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37192 grid for indexing accessible points = 1.400000 m= 43270 mr = 86311 m= 6143 mr = 31704 m= 267 mr = 3553 m= 2 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 245 time to turn everything in is 0.8400000 number of dielectric boundary points 46350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 331 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 35427 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5879730 object centre at (A) : 32.34400 21.43850 27.75950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7222268E-02 -2.0317908E-03 midg,1,midg; midg,igrid,midg 1.4557944E-02 1.3420568E-02 1,midg,midg; igrid,midg,midg -4.8884903E-03 1.5483895E-02 gauss-seidel spectral radius is 0.9986036 estimated iterations to convergence 212 setup time was (sec) 1.140000 now iterating at: 17:12:33 rms-change max change #iterations 5.268814 177.6513 at 10iterations 2.447718 65.30077 at 20iterations 1.137800 31.93497 at 30iterations 0.5298992 14.02603 at 40iterations 0.2470488 7.118385 at 50iterations 0.1150780 3.458031 at 60iterations 5.3943850E-02 1.537186 at 70iterations 2.5553966E-02 0.6579285 at 80iterations 1.2302495E-02 0.3306656 at 90iterations 6.2360233E-03 0.1611938 at 100iterations 3.4663328E-03 9.3894124E-02 at 110iterations 2.1598088E-03 6.0915828E-02 at 120iterations finished qdiffx linear iterations at : 17:12:39 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.1598088E-03 6.0915828E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 17:12:40 7.957u 0.161s 0:08.39 96.6% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 17:12:40 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4671 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.645879 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 2.923000 61.76500 ymin,ymax (A): -8.835000 51.71200 zmin,zma (A): -1.957000 57.47600 x,y,z range (A): 58.84200 60.54700 59.43300 scale (grids/A): 2.645879 object centre (A): 32.34400 21.43850 27.75950 number of atom coordinates read : 4671 total number of charged atoms : 4557 net assigned charge : -0.3649497 assigned positive charge : 723.6348 centred at (gu) : 84.52724 87.69935 90.82697 assigned negative charge : -724.0048 centred at (gu) : 84.12343 87.81377 90.62898 start vw surface at 0.2100000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 274388 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37192 grid for indexing accessible points = 1.400000 m= 141936 mr = 208777 m= 49062 mr = 116968 m= 10687 mr = 38734 m= 1244 mr = 7634 m= 54 mr = 757 m= 0 mr = 12 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 801 time to turn everything in is 2.140000 number of dielectric boundary points 104489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 36443 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.763919 object centre at (A) : 32.34400 21.43850 27.75950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3949326 0.2558514 midg,1,midg; midg,igrid,midg -0.1595753 -7.2379746E-02 1,midg,midg; igrid,midg,midg 3.7657812E-02 0.3127966 gauss-seidel spectral radius is 0.9992946 estimated iterations to convergence 297 setup time was (sec) 2.450000 now iterating at: 17:12:42 rms-change max change #iterations 12.87552 394.4259 at 10iterations 7.721514 151.7460 at 20iterations 4.610872 76.51567 at 30iterations 2.727047 49.05888 at 40iterations 1.611227 28.33957 at 50iterations 0.9503680 15.26128 at 60iterations 0.5575885 8.707268 at 70iterations 0.3269579 4.973010 at 80iterations 0.1919492 3.071848 at 90iterations 0.1124438 1.818998 at 100iterations 6.5871432E-02 0.9514503 at 110iterations 3.8631085E-02 0.5968800 at 120iterations 2.2690112E-02 0.3674784 at 130iterations 1.3381253E-02 0.1957645 at 140iterations 7.9798168E-03 0.1234150 at 150iterations 4.8625506E-03 8.7821662E-02 at 160iterations 3.0731889E-03 4.6735764E-02 at 170iterations 2.0493015E-03 3.3317566E-02 at 180iterations finished qdiffx linear iterations at : 17:12:53 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 2.0493015E-03 3.3317566E-02 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 17:12:54 13.478u 0.178s 0:13.96 97.7% 0+0k 0+0io 0pf+0w